view.aspects: View heatmap

Description Usage Arguments Value

View source: R/functions.R

Description

Internal function to visualize aspects of transcriptional heterogeneity as a heatmap. Used by pagoda.view.aspects.

Usage

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view.aspects(mat, row.clustering = NA, cell.clustering = NA, zlim = c(-1,
  1) * quantile(mat, p = 0.95), row.cols = NULL, col.cols = NULL,
  cols = colorRampPalette(c("darkgreen", "white", "darkorange"), space =
  "Lab")(1024), show.row.var.colors = TRUE, top = Inf, ...)

Arguments

mat

Numeric matrix

row.clustering

Row dendrogram

cell.clustering

Column dendrogram

zlim

Range of the normalized gene expression levels, inputted as a list: c(lower_bound, upper_bound). Values outside this range will be Winsorized. Useful for increasing the contrast of the heatmap visualizations. Default, set to the 5th and 95th percentiles.

row.cols

Matrix of row colors.

col.cols

Matrix of column colors. Useful for visualizing cell annotations such as batch labels.

cols

Heatmap colors

show.row.var.colors

Boolean of whether to show row variance as a color track

top

Restrict output to the top n aspects of heterogeneity

...

additional arguments for heatmap plotting

Value

A heatmap


hms-dbmi/scde documentation built on March 29, 2018, 1:23 p.m.